rs2282181

chr9-111371352-T-Cchr9-111371352-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364929.1(ECPAS):c.4737+269A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 152,188 control chromosomes in the GnomAD database, including 571 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.056 (571 hom., cov: 32)
• Consequence: ECPAS NM_001364929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

ECPAS (HGNC:29020): (Ecm29 proteasome adaptor and scaffold) Enables proteasome binding activity. Involved in ubiquitin-dependent ERAD pathway. Located in several cellular components, including centrosome; cytoplasmic vesicle; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ECPAS	NM_001364929.1	c.4737+269A>G		intron_variant		ENST00000684092.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECPAS	ENST00000684092.1	c.4737+269A>G		intron_variant			NM_001364929.1	P4
ECPAS	ENST00000259335.8	c.5271+269A>G		intron_variant		1
ECPAS	ENST00000338205.9	c.4737+269A>G		intron_variant		5		A1
ECPAS	ENST00000374383.1	c.168+269A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8457 AN: 152070 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0508

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0557 AC: 8477 AN: 152188 Hom.: 571 Cov.: 32 AF XY: 0.0541 AC XY: 4026 AN XY: 74402

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0257

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.00188

Gnomad4 NFE AF: 0.0118

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0375 Hom.: 68

Bravo AF: 0.0630

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.057
Dann	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2282181; hg19: chr9-114133632;